ChemoSpec: clupaSpectra – R documentation

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clupaSpectra

Hierarchical Cluster-Based Peak Alignment on a Spectra Object

Description

This function is a wrapper to several functions in the speaq package. It implements the CluPA algorithm described in the reference.

Usage

clupaSpectra(spectra, bT = NULL, ...)

Arguments

`spectra`	An object of S3 class `Spectra`.
`bT`	Numeric. The baseline threshold. Defaults to five percent of the range of the data, in `spectra$data`. Passed to `detectSpecPeaks`.
`...`	Other arguments to be passed to the underlying functions.

Value

A modifed Spectra object.

Author(s)

Bryan A. Hanson, DePauw University. hanson@depauw.edu

References

Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemiere F, Verschoren A, Goethals B, Laukens K. "An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data" BMC Bioinformatics vol. 12 pg. 405 (2011).

Examples

data(alignMUD)

plotSpectra(alignMUD,
  which = 1:20, lab.pos = 4.5, offset = 0.1,
  yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
  main = "Misaligned NMR Spectra (alignMUD)"
)

aMUD <- clupaSpectra(alignMUD)
plotSpectra(aMUD,
  which = 1:20, lab.pos = 4.5, offset = 0.1,
  yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
  main = "Aligned NMR Spectra (alignMUD)"
)

ChemoSpec

Exploratory Chemometrics for Spectroscopy

v5.3.11

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Mike Bostock [cph, ctb] (author of the d3.js library used by plotSpectraJS, http://d3js.org), Matt Keinsley [ctb] (author of initial AOV-PCA code)

Initial release

2021-03-24